Visualising Pathogen & Environmental Risk: transition to a user-ready toolkit (ViPER II)

Lead Research Organisation: University of Stirling
Department Name: Biological and Environmental Sciences

Abstract

Agricultural practices contribute a significant amount of faecal material onto pasture via direct defecation by grazing livestock and through applications of solid and liquid manures. Managing the spatial and temporal input of this faecal loading to pasture is important in order to minimise the proportion of faecal microorganisms, e.g. E. coli, that may be washed from faecal sources and transferred in runoff to nearby watercourses following rainfall. Contaminated runoff can lead to microbial pollution of our streams, rivers and seas. Scientists, environmental regulators, catchment managers and policy-makers are therefore keen to understand how E. coli survives and moves in the environment with a view that better knowledge and data on the behavioural characteristics of these microorganisms will improve our ability to model and predict their interactions with, and responses to, the world around us. The NERC-funded project ReMOFIO (NE/J004456/1) developed one such model to improve our understanding of the magnitude and spatial distribution of microbial risks in the landscape. The resulting ReMOFIO model predicts levels of microbial risk on agricultural land, based on livestock numbers, farming practices and E. coli survival patterns under environmental conditions (e.g. rainfall and temperature fluctuations). While the model is structurally simple its operation & functionality was not originally designed to maximise uptake by those who would benefit most from its use. In response, the original ViPER project used a participatory approach to bring together a range of stakeholders (regulators, catchment managers, scientists and farm networks) to promote engagement, deliberation and joint decision-making. Through a structured process of knowledge exchange the project team developed a freely-available prototype decision support tool (DST) called ViPER. The ViPER DST provides a user-friendly interface and allows end-users without specific modelling skills or knowledge of a modelling system to take advantage of existing NERC science and modelling capability (e.g. the ReMOFIO model) to understand how, when and where E. coli risks accumulate on agricultural land. However, in its current form, ViPER is unable to evaluate what proportion of that E. coli source on agricultural land will actually end up in rivers and streams following rainfall. In response, the aim of ViPER II is to now transition our prototype DST, which maps E. coli risks at the field, farm and catchment scale, into a user-ready toolkit for providing on-farm advice and guidance in the real world. To do this we will combine the ViPER DST with another freely-available NERC-funded hydrological risk-mapping tool called SCIMAP (NE/C508850/1). SCIMAP was designed to identify the origins of sediment and nutrient pollutants in the landscape and importantly, it maps how runoff can transfer sediment and nutrients across the soil surface and into watercourses. However, SCIMAP currently does not map microbial risks in the landscape because, unlike sediment and nutrients, bacteria such as E. coli accommodate a complex life-cycle and will die-off over time. By contrast, ViPER is able to account for the die-off of E. coli but lacks the capacity to predict E. coli transfer with runoff. An opportunity now exists to integrate two NERC-funded outputs (ViPER & SCIMAP) to deliver an innovative DST for mapping microbial pollution risks in catchment systems and to produce a DST that is greater than the sum of its individual parts. The resulting toolkit will provide added value both to land based assessment of microbial risks, and to the applied interests of environmental regulators and the water industry in the UK (& further afield). This represents the next critical step in ensuring that NERC funded models and data deliver real-world impact through innovative conversion of the underpinning evidence-base into a format that is widely accessible by relevant end-users.

Planned Impact

Making the most of research findings remains a major challenge for environmental scientists, regulators, decision-makers and those implementing policy. This is especially true in the field of catchment science where key advances in soil and water studies offer scope to transform the way in which land management is implemented to deliver multiple benefits, but which often remain inaccessible to those who would benefit most from their use. The core aims and objectives of our innovation project focus on exploiting the opportunities that arise from targeted stakeholder engagement & participatory methods during the co-construction of a decision-support tool, thus promoting access to NERC science & in turn maximising impact.

Immediate impact:
Implementation of this project will expand the role and visibility of the existing NERC funded science (covering multiple projects) on which the ViPER DST is built.

Short-term impact:
The KE model we propose is itself a key output and will facilitate much needed interaction among academic, regulator, water industry and catchment manager representatives. The establishment of the ViPER IDG to drive forward innovative and engaging ways to communicate NERC science linked to the exploration of microbial risks in agricultural systems should form a blue-print for good practice in KE. The approach will promote networking among project partners and academic researchers from across the UK.

Medium-term impact:
Our innovation project will deliver the ViPER II DST package - a freely available web-based portal that will provide an interface between existing NERC science and those interested in understanding the spatial and temporal patterns of microbial risks to land and water - principally the regulators and those with a responsibility for managing environmental risk. This will represent the most significant impact from our innovation efforts & will result in improved decision-making and the delivery of a practical tool for catchment management. This practical tool will represent the merging of science that has emerged from two NERC-funded projects. The ViPER DST will bridge the gap from scientific tool to user-friendly system for guiding decision making in agricultural catchments where diffuse microbial pollution from livestock farming is known to represent a key pressure on water quality. Importantly, to deliver this, we have proposed a pathway through which we can begin to embed the ViPER DST within everyday practice of farm advisors (e.g. those associated with Catchment Sensitive Farming, or SEPA awareness raising teams). Impact takes time to mature, and tools need to be accepted and taken up by end-users before converting to impact. Our proposal of participatory DST design and co-production of the ViPER framework, coupled with demonstration and training opportunities, will pave the way for efficient and effective impact from our innovation project.

Longer-term impact:
The project will deliver wider impacts for the general public too. The importance of microbial pollutants in catchments has been reinforced within the Water Framework Directive through the designation of 'protected areas', which are considered to be particularly sensitive to pollution or have particular economic, social or environmental importance. Bathing and shellfish harvesting waters, routinely monitored for faecal indicator organisms (FIOs), represent two types of 'protected areas' because of the potential for adverse effects on human health and the economy if contaminated with FIOs such as E. coli. The deployment of the ViPER DST in catchments prioritised as being significant contributors to FIO loading of bathing waters will ensure that advice is communicated to farm enterprises, both in the right way and at the right time, to help promote better livestock and manure management for cleaner and safer seas.

Publications

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Description The Visualising Pathogen & Environmental Risk (ViPER) project is a novel web-based decision support tool enabling access to a risk-based approach to modelling the burden of faecal indicator organisms (FIOs), e.g. E. coli, at the landscape scale. ViPER was developed at Stirling using NERC funding. In addition to NERC funding, the integration of new data into the design of ViPER from 2014 onwards has received in-kind funding contributions from the Scottish Environment Protection Agency (SEPA), Natural England, the Environment Agency (EA), the Drinking Water Quality Regulator (DWQR) for Scotland, United Utilities Ltd and Scottish Water, all of whom have played an active role in the co-design, development and customisation of the DST in order to deliver to their own, and wider, stakeholder needs.
NERC innovation funding, led by Stirling, developed the ViPER graphic user interface - a web-based portal for the model. The ViPER DST was further developed and integrated into SCIMAP, an existing risk-mapping tool designed to identify the origins of diffuse pollutants in the landscape through combined assessment of spatial patterns of source risks with hydrological connectivity, so that it became accessible to a wide range of end-users. This integration converted the preceding research into a new DST, SCIMAP-FIO.

The development of SCIMAP-FIO is innovative and scientifically novel because:
(i) it incorporates seasonal, field-relevant UK die-off rates for E. coli (which have been quantified by the Stirling team), thus removing any reliance on parameter values typically drawn from research undertaken in the USA and New Zealand due to a lack of UK data;
(ii) the underpinning E. coli source model that informs the ViPER DST has been tested at the headwater (0.5km2) through to catchment (574km2) scale to ascertain whether the E. coli die-off functions used are fit-for-purpose, and therefore our approach is associated with a degree of proven robustness that is not afforded to other DSTs of catchment scale FIO dynamics that simply assume that die-off rates correctly predict the source loading of FIOs in a catchment prior to their mobilisation;
(iii) specific modelling tools have been developed to complement SCIMAP-FIO, including the first freely-available E. coli calculator; a tool for calculating E. coli burden on pasture from grazing livestock as governed by faecal excretion and E. coli die-off. This supporting tool was specifically requested by stakeholders in the co-design phase of the DST;
(iv) it enabled an evaluation of the potential of the SCIMAP framework for handling microbial data with the first ever fit of E. coli data to predicted SCIMAP values, which utilised an extensive dataset provided by the Environment Agency;
(v) it was co-designed with relevant stakeholders during all stages of the DST development and application process - a series of participatory workshops allowed for end-user input into the functionality of the ultimate SCIMAP-FIO DST, together with an evaluation of the design process by stakeholders;
(vi) the end-product represents the first freely-available, web-accessible risk-based DST for mapping E. coli risks across agricultural catchments, and has been tested across two UK catchments using high resolution spatial data provided by the EA.
Exploitation Route Using a stakeholder-driven approach to develop SCIMAP-FIO allowed us to foster strong scientist-stakeholder relationships and promote joint ownership of the DST. This resulted in the design of a credible and trusted toolkit and: (i) the exploitation and utilisation of both mature & newly emerging NERC science; (ii) efficiency in learning, and co-design of a DST to facilitate stakeholder engagement with NERC science; & (iii) quality two-way training opportunities between academic and end-user organisations to enable the long-term sustainability of new partnerships. WE see the following potential benefits:

- Benefits to the farm advisory community: Strong end-user support is evidenced by proposals by CSF in England to train their farm advisors, who deal with 16,000 farm holdings, in the use of SCIMAP-FIO;
- Benefits to decision-makers in policy and regulatory roles: Scottish Government Centre of Expertise for Water (CREW) phase II funding for microbial pollution modelling is currently on hold while the ViPER II project runs - CREW were in attendance at our February 2018 workshop in Durham;
- Benefits to the environment: SCIMAP-FIO is relevant to the EA's and SEPA's work on the Bathing Waters Directive and Catchment Sensitive Farming initiative because the model can predict not only which stretches of stream or river are at greatest risk from diffuse microbial pollution, but also where the likely critical source areas are (i.e. we can spatially target mitigation and management options);
- Open access: SCIMAP-FIO is an open-source GIS, freely available WebApp, with user-friendly visual interface. Training resources will be freely available at www.scimap.org.uk.
Sectors Agriculture, Food and Drink,Environment

 
Title SCIMAP-FIO 
Description [The drop down list to the question above is NONSENSE! Its all biological] Identifying land that is most vulnerable in terms of contributing microbial pollution to water allows spatially-targeted catchment management for improving water quality and safeguarding human health. Catchment managers and environmental regulators need robust tools to help prioritise investment of their resources for protecting socially and economically important downstream areas, such as bathing or shellfish harvesting waters. We have worked with stakeholders to co-design a decision support tool (DST) that can identify critical sources of E. coli pollution. The DST will be used by UK regulators (e.g. Environment Agency, SEPA) and farm advisors (Natural England and the Catchment Sensitive Farming (CSF) teams) to assess the risk of microbial pollution within catchments. Impacts therefore include benefits to (i) the farm advisory community; (ii) decision-makers in policy and regulatory roles; and (iii) the environment through spatial targeting of mitigation and management. 
Type Of Material Improvements to research infrastructure 
Year Produced 2018 
Provided To Others? Yes  
Impact The tool was made available in October 2018; we are now in the process of monitoring uptake but impact will take time to mature. 
URL http://fio.scimap.org.uk
 
Description PI Oliver Fellowship funded by the OECD to spend 2 months in US department for Agriculture 
Organisation U.S. Department of Agriculture USDA
Country United States 
Sector Public 
PI Contribution Ongoing work of ViPER in terms of visualising and understanding risks of pathogens in agricultural systems is of interest to the USDA. Linked to this work the USDA invited me to apply for a 2 month visit to develop further links. My application was successful for a visit in July & August, 2018, funded by the OECD.
Collaborator Contribution The USDA supported the application and invited me to apply to spend time in their organisation.
Impact No outputs yet. Yes the collaboration is multidisciplinary (hydrology, microbiology, science-policy interface, catchment science)
Start Year 2018
 
Title SCIMAP-FIO 
Description Identifying land that is most vulnerable in terms of contributing microbial pollution to water allows spatially-targeted catchment management for improving water quality and safeguarding human health. Catchment managers and environmental regulators need robust tools to help prioritise investment of their resources for protecting socially and economically important downstream areas, such as bathing or shellfish harvesting waters. We have worked with stakeholders to co-design a decision support tool (DST) that can identify critical sources of E. coli pollution. The DST will be used by UK regulators (e.g. Environment Agency, SEPA) and farm advisors (Natural England and the Catchment Sensitive Farming (CSF) teams) to assess the risk of microbial pollution within catchments. Impacts therefore include benefits to (i) the farm advisory community; (ii) decision-makers in policy and regulatory roles; and (iii) the environment through spatial targeting of mitigation and management. 
Type Of Technology Webtool/Application 
Year Produced 2018 
Open Source License? Yes  
Impact The DST was launched in October 2018; we are monitoring uptake and promoting its availability among end-users - impact will take time to now bed in and mature. 
URL http://fio.scimap.org.uk
 
Description Natural England Webinar to Catchment Sensitive Farming Officers 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact D Oliver participated in a Natural England Webinar, which included the Environment Agency Bathing Water lead also, in early January to inform the Catchment Sensitive Farming (CSF) team about SCIMAP-FIO. CSF are considering whether the tool and its outputs can be included in the CSF evidence prospectus. CSF asked for risk maps for the Porth and Porthluney catchments in Cornwall to be produced and presented at the webinar. The CSF officer in Cornwall said the risk maps revealed patterns as he would expect. As a result, that catchment officer said it would be good to run the tool for catchments nationally across England - thus highlighting interest in our decision support tool. Approximately 40 CSF officers were logged in to the webinar.
Year(s) Of Engagement Activity 2019
 
Description SCIMAP-FIO launch and user group meetng 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact In September 2018, 24 participants attended the 2018 SCIMAP User Group meeting at Birmingham, which included the launch of SCIMAP-FIO. The launch generated interest across the end-user community in the use of our risk mapping tool now that it the approach had been finalised.
Year(s) Of Engagement Activity 2018
URL http://fio.scimap.org.uk
 
Description ViPER2 Inception workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Inception workshop to help co-design a decision support tool
Year(s) Of Engagement Activity 2017
 
Description Viper2 steering workshop 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Mid-project steering group workshop to guide decision support tool developments
Year(s) Of Engagement Activity 2018